The risk of gene flow and the possible ecological environmental effects of the transgenic crops are the important contents of the safety assessment which is a necessary link before the commercialization. For assessing the genetic flow risk of Glyphosate-Tolerate Soybean S4003.12 and S4003.14, the germination rate of pollen in profuse flowering seasons from transgenic soybean, its receptor and conventional cultivated soybean varieties which selected in the greenhouses were detected by fluid nutrient medium, and the diameter of pollen grains were observed under scale microscope. The results showed that pollen germination rate of soybean was strongest when the pollen just in vitro which approximately 88.2% after 2 h. The germination vigor of the pollen decreased with the lengthening of the time in vitro, the pollen was almost completely inactivated when put it at room temperature for 3 h. No significant effect on the viability of pollen in vitro and the diameter of pollen grains between the Glyphosate-Tolerate Soybean S4003.12, S4003.14 and the normal control. The study showed that there was no significant difference between the pollen transmission ability of glyphosate resistant transgenic soybean and non transgenic soybean and the risk of extraneous gene escape could be effectively avoided by setting the isolation zone.